http://lod.bco-dmo.org/id/dataset/716806
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-10-12
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Reef Fish genetic accessions at NCBI Genbank from samples collected in the Indian Ocean, Pacific Ocean, and Red Sea from 2005 to 2015; related to 2016 publications
2017-12-18
publication
2017-12-18
revision
BCO-DMO Linked Data URI
2017-12-18
creation
http://lod.bco-dmo.org/id/dataset/716806
Brian Bowen
University of Hawaiʻi at Mānoa
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Bowen, B. (2017) Reef Fish genetic accessions at NCBI Genbank from samples collected in the Indian Ocean, Pacific Ocean, and Red Sea from 2005 to 2015; related to 2016 publications. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-12-18 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/716806 [access date]
Genetic accessions at NCBI Genbank Dataset Description: <p>This dataset contains&nbsp;GenBank&nbsp;accession numbers for various genomic and mtDNA loci&nbsp;sequences from reef fish.&nbsp; The fish were sampled in multiple locations in the Indian Ocean, Pacific Ocean, and&nbsp;the Red Sea between 2005 to 2015.&nbsp;&nbsp;</p>
<p><strong>These data were published in&nbsp;the data sections of the following publications:</strong></p>
<p>Coleman, R.R., J.A. Eble, J.D. DiBattista, L.A. Rocha, J.E. Randall, M.L. Berumen, B.W. Bowen. 2016. Regal phylogeography:&nbsp;range-wide&nbsp;survey of the marine angelfish&nbsp;Pygoplites&nbsp;diacanthus&nbsp;reveals evolutionary partitions between the Red Sea, Indian Ocean, and&nbsp;Pacific Ocean. Molecular Phylogenetics and Evolution 100:243 – 253. doi: <a href="http://dx.doi.org/10.1016/j.ympev.2016.04.005" target="_blank">10.1016/j.ympev.2016.04.005</a>.</p>
<p>DiBattista J.D., J. Whitney, M.T. Craig, J.-P. A. Hobbs, L.A. Rocha, K.A. Feldheim, M.L. Berumen, B.W. Bowen. 2016. Surgeons and suture zones: hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes. Molecular Phylogenetics and Evolution 101:203 – 215. doi: <a href="http://dx.doi.org/10.1016/j.ympev.2016.04.036" target="_blank">10.1016/j.ympev.2016.04.036</a>.</p>
<p>DiBattista, J.D., M.R. Gaither, J.-P. A. Hobbs, L.A. Rocha, B.W. Bowen. 2016. Angelfishes, paper tigers, and the devilish taxonomy of the&nbsp;Centropyge&nbsp;flavissima&nbsp;complex. Journal of Heredity 107:647 – 653. doi: <a href="http://dx.doi.org/10.1093/jhered/esw062" target="_blank">10.1093/jhered/esw062</a>.</p>
<p>Tenggardjaja, K. A., Bowen, B. W., &amp; Bernardi, G. (2014). Vertical and horizontal genetic connectivity in Chromis verater, an endemic damselfish found on shallow and mesophotic reefs in the Hawaiian Archipelago and adjacent Johnston Atoll.&nbsp;<em>PLoS One</em>,&nbsp;<em>9&nbsp;</em>(12), e115493. doi:&nbsp;<a href="https://doi.org/10.1371/journal.pone.0115493" target="_blank">10.1371/journal.pone.0115493</a></p>
<p>Tenggardjaja, K.A., B.W. Bowen, G. Bernardi. 2016. Reef fish dispersal in the Hawaiian Archipelago: comparative phylogeography of three endemic damselfishes. Journal of Marine Biology: Article ID 3251814. doi: <a href="http://dx.doi.org/10.1155/2016/3251814" target="_blank">10.1155/2016/3251814</a>.</p> Methods and Sampling: <p><strong>Methodology:&nbsp;</strong>Various genomic and mtDNA loci were sequenced from reef fishes.</p>
<p><strong>Sampling and analytical procedures:&nbsp;</strong>Samples were taken as fine clips, then sequenced and analyzed to detect population structure and evolutionary genetic divergences. Species were collected with scuba gear, nets, and spears.&nbsp;</p>
<p>Raw sequence data&nbsp;was&nbsp;aligned with GENEIOUS R6 (Biomatters, LTD, Auckland, NZ) or GENEIOUS v.8.0.3 (Gene Codes, Ann Arbor, MI, USA). Sequence analyses were performed with BEAST v.2.2.0 and ARLEQUIN v. 3.5.</p>
<p>For details of these analyses, see the references listed in the "Description" section of this page.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1558852 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1558852
completed
Brian Bowen
University of Hawaiʻi at Mānoa
808-236-7426
Hawaii Institute of Marine Biology 46-007 Lilipuna Road
Kaneohe
HI
96744
USA
bbowen@hawaii.edu
pointOfContact
asNeeded
Unknown
Species_Names
Sequence_Description
Collection_Location
Sequence_Analysis_Method
Genbank_Accession_Range
Genbank_First_Accession_Link
Collection_Max_Lat
Collection_Min_Lat
Collection_Max_Lon
Collection_Min_Lon
Journal_Publications
Journal_Publication_DOI
ABI 3730XL Genetic Analyzer
theme
None, User defined
taxon
sample description
site
instrument
accession number
external_link
latitude
longitude
reference_paper
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Indo-Pac Research Coordination Network
https://indopacificnetwork.wikispaces.com/
Indo-Pac Research Coordination Network
Description from NSF award abstract:
The objective of this Research Coordination Network project is to develop an international network of researchers who use genetic methodologies to study the ecology and evolution of marine organisms in the Indo-Pacific to share data, ideas and methods. The tropical Indian and Pacific Oceans encompass the largest biogeographic region on the planet, the Indo-Pacific. It spans over half of the Earth's circumference and includes the exclusive economic zones of over 50 nations and territories. The Indo-Pacific is also home to our world's most diverse marine environments. The enormity and diversity of the Indo-Pacific poses tremendous logistical, political and financial obstacles to individual researchers and laboratories attempting to study the marine biology of the region. Genetic methods can provide invaluable information for our understanding of processes ranging from individual dispersal to the composition and assembly of entire marine communities.
The project will:
(1) assemble a unique, open access database of population genetic data and associated metadata that is compatible with the developing genomic and biological diversity standards for data archiving,
(2) facilitate open communication and collaboration among researchers from across the region through international workshops, virtual communication and a collaborative website,
(3) promote training in the use of genetic methodologies in ecology and evolution for researchers from developing countries through these same venues, and
(4) use the assembled database to address fundamental questions about the evolution of species and the reservoirs of genetic diversity in the Indo-Pacific.
The network will provide a model for international collaborative networks and genetic databasing in biodiversity research that extends beyond the results of this Research Coordination Network effort.
Indo-Pac RCN
largerWorkCitation
program
Origins of Hawaiian Reef Fishes
https://osprey.bco-dmo.org/project/635745
Origins of Hawaiian Reef Fishes
<p><em>Project summary:</em><br />
This research is designed to resolve the origins of Hawaiian reef fishes. All living inhabitants of the Hawaiian archipelago necessarily originate elsewhere, due to the volcanic history of the island arc. Hawaii also has the highest endemism (native species) in the Pacific, with 25% of the 625 near-shore fish species found nowhere else. Where did these fishes come from? Two prominent hypotheses regarding the origins of Hawaiian marine species maintain that colonists arrive either from the south (via the Line Islands and Johnston Atoll) or from the west (via Japan). Previous research has shown that Hawaiian endemic limpets (genus <em>Cellana</em>) colonized from Japan (Bird et al. 2011 Mol. Ecol. 20:2128 – 2141). Andrews et al. (2014; PLoS One 9: e91665) report evidence for a colonization pathway from the south (Johnston Atoll) to the middle of the archipelago in the Papahanaumokuakea Marine National Monument (PMNM). In this project, we will sample locations to the south of Hawaii (Johnston and Line Islands) and to the west of Hawaii (Ogasawara and Ryukyu Islands) for a suite of 20 reef fishes in order to resolve the origins of Hawaiian biodiversity. Advanced rebreather technology allows dives with longer bottom time and more efficient sample collection, and our program is pioneering the applications of this advance diving technology. To test alternate hypotheses in the lab, we will employ both population genetics (shifts in genotype frequencies) and phylogenetics (DNA sequence divergence) for more ancient separations. Restriction-digest associated DNA sequencing (RAD-seq) is the best method for studies of phylogeography, phylogenetics, and population biology because it provides high coverage of homologous portions of the genome from multiple individuals for comparatively low cost and effort. We use the ezRAD approach developed in the shared Bowen-Toonen Lab.</p>
<p><strong>Description from NSF award abstract:</strong><br />
The Hawaiian Islands are the product of a volcanic hot spot in the middle of the North Pacific. Hence every living thing on this isolated archipelago has origins elsewhere. This project will investigate the origins of Hawaiian reef fishes, which are important both as a food source and a cultural touchstone in native Hawaiian communities. Two prominent hypotheses maintain that marine fish originally arrived from the south (Line Islands and Johnston Atoll) or from the west (Japan). To test these hypotheses, this research will augment existing specimens from Hawaii with expeditions to Johnston Atoll (closest shallow habitat to the south), the northern Line Islands (Palmyra), southern Line Islands (Christmas Island), and Ryukyu Islands and Ogasawara Islands in Japan. Advanced genetic techniques will be used to resolve the closest relatives to the Hawaiian fish species and the pathways by which reef species colonize Hawaii and help establish patterns of biodiversity. In cases where Hawaiian species are closely related to widespread sister species, this project will detect hotspots of genetic divergence. Because this research will reveal the sources of Hawaiian marine biodiversity, results can be used to help define priorities for reef protection. The project will support two graduate students and train at least two more in all aspects of the project from rebreather diving, specimen collection and curation, information management, and advanced genetic techniques. There will be outreach efforts to schools through existing programs, and expedition teams will include a videographer to provide footage for the award-winning Voice of the Sea program, broadcast locally. Expeditions will also include an outreach specialist to handle media reports and promote awareness and concern for reefs in the communities surrounding study sites. </p>
<p>The investigators will sample a suite of 20 reef fishes at locations to the south (Johnston and Line Islands) and west (Ogasawara and Ryukyu Islands) of Hawaii to resolve the origins of Hawaiian biodiversity. The investigators will employ both population genetics (shifts in genotype frequencies) and phylogenetics (DNA sequence divergence) for more ancient separations to test their hypotheses. Restriction-digest associated DNA sequencing (RAD-seq) will be employed for the phylogeography, phylogenetics, and population biology studies because it provides high coverage of homologous portions of the genome from multiple individuals for comparatively low cost and effort.</p>
Hawaiian Fish Origins
largerWorkCitation
project
eng; USA
oceans
-180
35
-20
30
2017-12-18
Central and West Pacific Ocean
0
BCO-DMO catalogue of parameters from Reef Fish genetic accessions at NCBI Genbank from samples collected in the Indian Ocean, Pacific Ocean, and Red Sea from 2005 to 2015; related to 2016 publications
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/721373.rdf
Name: Species_Names
Units: unitless
Description: <p>Name of species sampled</p>
http://lod.bco-dmo.org/id/dataset-parameter/721374.rdf
Name: Sequence_Description
Units: unitless
Description: <p>Description of type of sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/721375.rdf
Name: Collection_Location
Units: unitless
Description: <p>Location species were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/721376.rdf
Name: Sequence_Analysis_Method
Units: unitless
Description: <p>Sequence method and instrument</p>
http://lod.bco-dmo.org/id/dataset-parameter/721377.rdf
Name: Genbank_Accession_Range
Units: unitless
Description: <p>Range of accession numbers at National Center for Biotechnology Information (NCBI) Genbank</p>
http://lod.bco-dmo.org/id/dataset-parameter/721378.rdf
Name: Genbank_First_Accession_Link
Units: unitless
Description: <p>Link to the first accession in the accession range at National Center for Biotechnology Information (NCBI) Genbank</p>
http://lod.bco-dmo.org/id/dataset-parameter/721379.rdf
Name: Collection_Max_Lat
Units: decimal degrees
Description: <p>Maximum species collection latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/721380.rdf
Name: Collection_Min_Lat
Units: decimal degrees
Description: <p>Minimum species collection latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/721381.rdf
Name: Collection_Max_Lon
Units: decimal degrees
Description: <p>Maximum species collection longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/721382.rdf
Name: Collection_Min_Lon
Units: decimal degrees
Description: <p>Minimum species collection longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/721383.rdf
Name: Journal_Publications
Units: untiless
Description: <p>Journal publications these accessions were published in</p>
http://lod.bco-dmo.org/id/dataset-parameter/721384.rdf
Name: Journal_Publication_DOI
Units: untiless
Description: <p>Digital object identifier (DOI) for the journal publications these accessions were published in</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2852
https://datadocs.bco-dmo.org/file/7DDMm1Mfmy9VYN/accessions.csv
accessions.csv
Primary data file for dataset ID 716806
download
https://osprey.bco-dmo.org/dataset/716806/data/download
download
onLine
dataset
<p><strong>Methodology:&nbsp;</strong>Various genomic and mtDNA loci were sequenced from reef fishes.</p>
<p><strong>Sampling and analytical procedures:&nbsp;</strong>Samples were taken as fine clips, then sequenced and analyzed to detect population structure and evolutionary genetic divergences. Species were collected with scuba gear, nets, and spears.&nbsp;</p>
<p>Raw sequence data&nbsp;was&nbsp;aligned with GENEIOUS R6 (Biomatters, LTD, Auckland, NZ) or GENEIOUS v.8.0.3 (Gene Codes, Ann Arbor, MI, USA). Sequence analyses were performed with BEAST v.2.2.0 and ARLEQUIN v. 3.5.</p>
<p>For details of these analyses, see the references listed in the "Description" section of this page.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Data Manager Processing Notes:<br />
* added a conventional header with dataset name, PI name, version date<br />
* modified parameter names to conform with BCO-DMO naming conventions<br />
* added columns for max/min latitude and longitudes for species collections<br />
* added column with DOIs for the journal references<br />
* modified dataset so each row contains one range of accessions.<br />
* replaced commas in the data with semicolons to support .csv format of data</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
ABI 3730XL Genetic Analyzer
ABI 3730XL Genetic Analyzer
PI Supplied Instrument Name: ABI 3730XL Genetic Analyzer PI Supplied Instrument Description:ABI 3730XL Genetic Analyzer (Applied Biosystems, Foster City, CA, USA) Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.